The length of time an idea or system of beliefs has been around is no guide to the correctness of the idea or system.
For example, take the 'four humors' view of medicine and disease. It was around for thousands of years and extensively used. But it was simply wrong. It was based on some observations that were made long before we had techniques or instruments for more valid results. And once those techniques and instruments were invented, that theory went away.
I could also point to the 'four elements' idea of the composition of matter, the geocentric universe, alchemy, astrology and other ancient ideas that are known to simply be wrong today, yet were accepted for thousands of years.
More specifically, in regards to the ideas relating to spirituality, the concept is that these ideas were the result of speculation and observation done at a rather primitive state of knowledge and are *less* likely to be correct because of that. When more detailed observations have been made, many of the things promoted by 'spiritual' reasoning have found to be wanting or simply wrong.
Another aspect is that the scientific outlook searches for *objective* statements and subjects them to testing to sure they work, actually attempting to prove the ideas *wrong* and seeing what is left over. The goal is to eliminate falsehoods.
On the other side, spiritual paths tend to emphasize 'faith', which is a subjective thing and varies from individual to individual. Challenging the faith by trying to show it is wrong is strongly discouraged.
But what we KNOW is that humans and human intuition are very, very poor at finding general truths. We make mistakes. We adhere to ideas that comfort us. We get egos involved. And that means that any ideas *need* to be challenged in a way that is precisely counter to the concept of faith as a positive value.